VMD-L Mailing List

From: Jeffery (ytseng3_at_uic.edu)
Date: Mon Jan 31 2005 - 14:59:52 CST

Thanks for your quick response.

Yes, couple of reasons.

1. We want to focus on a local region of protein and this region is
different from a protein to another protein.

 It seams "global_matrix" is doing this job "transforming the a specific
position "x,y,z" to center of the screen, which is what we want.

However, we have no idea what's the relationship among "global_ matrix" and
"rotate_matrix" , "scale_matrix".
More important, how do you calculate "global_matrix"?

But I suspect that the global_matrix = rotate_matrix/scale_matrix.
If this is correct, is there any builtin function doing "/" ?

2. If using built_in commands like "rotate x to/by", it is unlikely to
render pictures from "topview", "centerview" and "rightview" , because it
can not apply "automatically" to ALL molecules we feel interested at.

However, through the global_matrix, we can make it for focusing on the
local region we want.

For example : find the center of the protein pocket.

then we could find the center of the local region by "measure" and move it
the center of screen.

 vmd > set sel [atomselect top {poc43}]
# poc43 is the marco that we pre_defined

## measure the center
vmd > set M [measure center $sel weight mass]
.....

### apply it to global_matrix

The next step, by rotate_matrix, I expect that we could render the local
regions from "topview, centerview and rightview"

But how do you assign the values into "rotate_matrix" to get 3 different
viewpoints.

It is unlikely to use "rotate x to/by" to achieve the purposes for ALL the
protein "automatically".
but there are some chances through "global_matrix".

Thanks,

-Jeffrey

>
> Jeffrey,
> You might find it much easier to apply rotations like these
> using combinations of "rotate x to" and "rotate y by" commands.
> That'd be much easier than directly forming the global matrix
> for yourself. Let me know if there's some reason you're unable
> to use the built-in rotate commands for this purpose.
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Mon, Jan 31, 2005 at 02:18:02PM -0600, Jeffery wrote:
> > Hi, All
> >
> >
> > Dose anyone know how to calculate "global_matrix" defined in VMD?
> >
> > and
> >
> > If we want to "automatically" render pictures from three different
viewpoints of molecules, say from topview, centerview, rightview, how could
we make it by assigning values of "rotate_matrix" defined in VMD ?
> >
> >
> >
> > Thanks,
> > Jeffrey Tseng
> >
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>